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Unable to install on fresh python env #77

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mkolopanis opened this issue Oct 28, 2021 · 3 comments
Open

Unable to install on fresh python env #77

mkolopanis opened this issue Oct 28, 2021 · 3 comments

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@mkolopanis
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It appears with the tagged version of scikit-image, there is no pyproject.toml to require a numpy package be installed before building.
As a result, a user is required to install numpy into their environment before attempting to install this package.
Even defining a minimal pyroject.toml here like below cannot alleviate the issue.

[build-system]
requires = ["setuptools>=30.3.0", "wheel", "numpy==1.19.5"]

However bumping to scikit-image==0.18.0 does appear to fix the issue.
Can't guarantee tests will pass with this version since they appear to already not pass as of 5aaf81f however the three that are passing on the main branch also still pass

Blank Env Install 
(base) mkolopanis@enterprise [12:35:52] [~/src] 
-> % mamba create -n dora python=3.9

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.15.3) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['python=3.9']

pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) Done
pkgs/main/linux-64       [====================] (00m:01s) Done
conda-forge/noarch       [====================] (00m:02s) Done
conda-forge/linux-64     [====================] (00m:05s) Done
Transaction

  Prefix: /home/mkolopanis/src/anaconda/envs/dora

  Updating specs:

   - python=3.9


  Package                Version  Build           Channel                  Size
─────────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex            0.1  main            pkgs/main/linux-64     Cached
  + _openmp_mutex            4.5  1_gnu           pkgs/main/linux-64     Cached
  + ca-certificates   2021.10.26  h06a4308_2      pkgs/main/linux-64     115 KB
  + certifi            2021.10.8  py39h06a4308_0  pkgs/main/linux-64     151 KB
  + ld_impl_linux-64      2.35.1  h7274673_9      pkgs/main/linux-64     Cached
  + libffi                   3.3  he6710b0_2      pkgs/main/linux-64     Cached
  + libgcc-ng              9.3.0  h5101ec6_17     pkgs/main/linux-64     Cached
  + libgomp                9.3.0  h5101ec6_17     pkgs/main/linux-64     Cached
  + libstdcxx-ng           9.3.0  hd4cf53a_17     pkgs/main/linux-64     Cached
  + ncurses                  6.2  he6710b0_1      pkgs/main/linux-64     Cached
  + openssl               1.1.1l  h7f8727e_0      pkgs/main/linux-64     Cached
  + pip                   21.2.4  py39h06a4308_0  pkgs/main/linux-64       2 MB
  + python                 3.9.7  h12debd9_1      pkgs/main/linux-64     Cached
  + readline                 8.1  h27cfd23_0      pkgs/main/linux-64     Cached
  + setuptools            58.0.4  py39h06a4308_0  pkgs/main/linux-64     Cached
  + sqlite                3.36.0  hc218d9a_0      pkgs/main/linux-64     Cached
  + tk                    8.6.11  h1ccaba5_0      pkgs/main/linux-64     Cached
  + tzdata                 2021e  hda174b7_0      pkgs/main/noarch       112 KB
  + wheel                 0.37.0  pyhd3eb1b0_1    pkgs/main/noarch       Cached
  + xz                     5.2.5  h7b6447c_0      pkgs/main/linux-64     Cached
  + zlib                  1.2.11  h7b6447c_3      pkgs/main/linux-64     Cached

  Summary:

  Install: 21 packages

  Total download: 2 MB

─────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y
Finished tzdata                               (00m:00s)             112 KB      1 MB/s
Finished certifi                              (00m:00s)             151 KB      1 MB/s
Finished ca-certificates                      (00m:00s)             115 KB    939 KB/s
Finished pip                                  (00m:00s)               2 MB     13 MB/s
Downloading  [==================================================================] (00m:03s)   14.80 MB/s
Extracting   [==================================================================] (00m:02s)        4 / 4
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate dora
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(dora) mkolopanis@enterprise [12:37:32] [~/src/dora] [master]
-> % pip install .
Processing /data4/mkolopanis/src/dora
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting scikit-image==0.17.2
  Downloading scikit-image-0.17.2.tar.gz (29.8 MB)
     |████████████████████████████████| 29.8 MB 87 kB/s 
    ERROR: Command errored out with exit status 1:
     command: /home/mkolopanis/src/anaconda/envs/dora/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a54gexg8/scikit-image_76e676b8e7f64e3984be8a4a56f1be28/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a54gexg8/scikit-image_76e676b8e7f64e3984be8a4a56f1be28/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-g94udfeq
         cwd: /tmp/pip-install-a54gexg8/scikit-image_76e676b8e7f64e3984be8a4a56f1be28/
    Complete output (7 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-a54gexg8/scikit-image_76e676b8e7f64e3984be8a4a56f1be28/setup.py", line 234, in <module>
        'build_ext': openmp_build_ext(),
      File "/tmp/pip-install-a54gexg8/scikit-image_76e676b8e7f64e3984be8a4a56f1be28/setup.py", line 58, in openmp_build_ext
        from numpy.distutils.command.build_ext import build_ext
    ModuleNotFoundError: No module named 'numpy'
    ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/54/fd/c1b0bb8f6f12ef9b4ee8d7674dac82cd482886f8b5cd165631efa533e237/scikit-image-0.17.2.tar.gz#sha256=bd954c0588f0f7e81d9763dc95e06950e68247d540476e06cb77bcbcd8c2d8b3 (from https://pypi.org/simple/scikit-image/) (requires-python:>=3.6). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Could not find a version that satisfies the requirement scikit-image==0.17.2 (from dora-exp-pipeline) (from versions: 0.7.2, 0.8.0, 0.8.1, 0.8.2, 0.9.0, 0.9.1, 0.9.3, 0.10.0, 0.10.1, 0.11.2, 0.11.3, 0.12.0, 0.12.1, 0.12.2, 0.12.3, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.14.2, 0.14.3, 0.14.5, 0.15.0, 0.16.2, 0.17.1, 0.17.2, 0.18.0rc0, 0.18.0rc1, 0.18.0rc2, 0.18.0, 0.18.1, 0.18.2rc1, 0.18.2rc2, 0.18.2, 0.18.3)
ERROR: No matching distribution found for scikit-image==0.17.2
Env w/ Numpy 
(dora) mkolopanis@enterprise [12:45:38] [~/src/dora] [master *]
-> % mamba install numpy==1.19.5    

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.15.3) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['numpy==1.19.5']

conda-forge/linux-64     Using cache
conda-forge/noarch       Using cache
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change

Pinned packages:
  - python 3.9.*


Transaction

  Prefix: /home/mkolopanis/src/anaconda/envs/dora

  Updating specs:

   - numpy==1.19.5
   - ca-certificates
   - certifi
   - openssl


  Package           Version  Build                Channel                    Size
───────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────

  + libblas           3.9.0  11_linux64_openblas  conda-forge/linux-64     Cached
  + libcblas          3.9.0  11_linux64_openblas  conda-forge/linux-64     Cached
  + libgfortran-ng    9.3.0  ha5ec8a7_17          pkgs/main/linux-64       Cached
  + libgfortran5      9.3.0  ha5ec8a7_17          pkgs/main/linux-64       Cached
  + liblapack         3.9.0  11_linux64_openblas  conda-forge/linux-64     Cached
  + libopenblas      0.3.17  pthreads_h8fe5266_1  conda-forge/linux-64     Cached
  + numpy            1.19.5  py39hdbf815f_2       conda-forge/linux-64       5 MB
  + python_abi          3.9  2_cp39               conda-forge/linux-64     Cached

  Summary:

  Install: 8 packages

  Total download: 5 MB

───────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y
Finished numpy                                (00m:00s)               5 MB      5 MB/s
Downloading  [==================================================================] (00m:05s)    4.80 MB/s
Extracting   [==================================================================] (00m:00s)        1 / 1
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(dora) mkolopanis@enterprise [12:46:10] [~/src/dora] [master *]
-> % pip install .
Processing /data4/mkolopanis/src/dora
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting rasterio==1.2.6
  Downloading rasterio-1.2.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (19.2 MB)
     |████████████████████████████████| 19.2 MB 15.2 MB/s 
Collecting PyYAML==5.4.1
  Downloading PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl (630 kB)
     |████████████████████████████████| 630 kB 20.7 MB/s 
Collecting Pillow==8.2.0
  Downloading Pillow-8.2.0-cp39-cp39-manylinux1_x86_64.whl (3.0 MB)
     |████████████████████████████████| 3.0 MB 34.9 MB/s 
Collecting tensorflow-addons==0.13.0
  Downloading tensorflow_addons-0.13.0-cp39-cp39-manylinux2010_x86_64.whl (679 kB)
     |████████████████████████████████| 679 kB 21.2 MB/s 
Collecting sklearn-som==1.1.0
  Downloading sklearn_som-1.1.0-py3-none-any.whl (6.7 kB)
Collecting tensorflow==2.5.1
  Downloading tensorflow-2.5.1-cp39-cp39-manylinux2010_x86_64.whl (454.5 MB)
     |████████████████████████████████| 454.5 MB 31 kB/s 
Collecting scikit-learn==0.24.2
  Downloading scikit_learn-0.24.2-cp39-cp39-manylinux2010_x86_64.whl (23.8 MB)
     |████████████████████████████████| 23.8 MB 16.6 MB/s 
Collecting matplotlib==3.3.4
  Downloading matplotlib-3.3.4-cp39-cp39-manylinux1_x86_64.whl (11.5 MB)
     |████████████████████████████████| 11.5 MB 21.5 MB/s 
Requirement already satisfied: numpy==1.19.5 in /data4/mkolopanis/src/anaconda/envs/dora/lib/python3.9/site-packages (from dora-exp-pipeline==0.0.9) (1.19.5)
Collecting scipy==1.5.4
  Downloading scipy-1.5.4-cp39-cp39-manylinux1_x86_64.whl (25.8 MB)
     |████████████████████████████████| 25.8 MB 20.1 MB/s 
Collecting tqdm==4.62.0
  Downloading tqdm-4.62.0-py2.py3-none-any.whl (76 kB)
     |████████████████████████████████| 76 kB 10.5 MB/s 
Collecting pandas==1.1.5
  Downloading pandas-1.1.5-cp39-cp39-manylinux1_x86_64.whl (9.3 MB)
     |████████████████████████████████| 9.3 MB 22.5 MB/s 
Collecting tensorflow-probability==0.13.0
  Downloading tensorflow_probability-0.13.0-py2.py3-none-any.whl (5.4 MB)
     |████████████████████████████████| 5.4 MB 23.8 MB/s 
Collecting scikit-image==0.17.2
  Using cached scikit-image-0.17.2.tar.gz (29.8 MB)
Collecting planetaryimage==0.5.0
  Downloading planetaryimage-0.5.0-py2.py3-none-any.whl (13 kB)
Collecting python-dateutil>=2.1
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
     |████████████████████████████████| 247 kB 22.5 MB/s 
Collecting cycler>=0.10
  Downloading cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting kiwisolver>=1.0.1
  Downloading kiwisolver-1.3.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
     |████████████████████████████████| 1.6 MB 22.3 MB/s 
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Downloading pyparsing-3.0.3-py3-none-any.whl (96 kB)
     |████████████████████████████████| 96 kB 11.4 MB/s 
Collecting pytz>=2017.2
  Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB)
     |████████████████████████████████| 503 kB 29.0 MB/s 
Collecting six
  Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pvl
  Downloading pvl-1.3.0-py2.py3-none-any.whl (65 kB)
     |████████████████████████████████| 65 kB 7.7 MB/s 
Collecting click>=4.0
  Downloading click-8.0.3-py3-none-any.whl (97 kB)
     |████████████████████████████████| 97 kB 12.9 MB/s 
Collecting click-plugins
  Downloading click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB)
Requirement already satisfied: certifi in /data4/mkolopanis/src/anaconda/envs/dora/lib/python3.9/site-packages (from rasterio==1.2.6->dora-exp-pipeline==0.0.9) (2021.10.8)
Requirement already satisfied: setuptools in /data4/mkolopanis/src/anaconda/envs/dora/lib/python3.9/site-packages (from rasterio==1.2.6->dora-exp-pipeline==0.0.9) (58.0.4)
Collecting snuggs>=1.4.1
  Downloading snuggs-1.4.7-py3-none-any.whl (5.4 kB)
Collecting attrs
  Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB)
     |████████████████████████████████| 53 kB 6.5 MB/s 
Collecting affine
  Downloading affine-2.3.0-py2.py3-none-any.whl (15 kB)
Collecting cligj>=0.5
  Downloading cligj-0.7.2-py3-none-any.whl (7.1 kB)
Collecting networkx>=2.0
  Downloading networkx-2.6.3-py3-none-any.whl (1.9 MB)
     |████████████████████████████████| 1.9 MB 20.6 MB/s 
Collecting imageio>=2.3.0
  Downloading imageio-2.10.1-py3-none-any.whl (3.3 MB)
     |████████████████████████████████| 3.3 MB 15.7 MB/s 
Collecting tifffile>=2019.7.26
  Downloading tifffile-2021.10.12-py3-none-any.whl (175 kB)
     |████████████████████████████████| 175 kB 15.4 MB/s 
Collecting PyWavelets>=1.1.1
  Downloading PyWavelets-1.1.1-cp39-cp39-manylinux1_x86_64.whl (4.3 MB)
     |████████████████████████████████| 4.3 MB 15.1 MB/s 
Collecting threadpoolctl>=2.0.0
  Downloading threadpoolctl-3.0.0-py3-none-any.whl (14 kB)
Collecting joblib>=0.11
  Downloading joblib-1.1.0-py2.py3-none-any.whl (306 kB)
     |████████████████████████████████| 306 kB 15.8 MB/s 
Collecting six
  Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting termcolor~=1.1.0
  Downloading termcolor-1.1.0.tar.gz (3.9 kB)
Collecting gast==0.4.0
  Downloading gast-0.4.0-py3-none-any.whl (9.8 kB)
Collecting absl-py~=0.10
  Downloading absl_py-0.15.0-py3-none-any.whl (132 kB)
     |████████████████████████████████| 132 kB 17.4 MB/s 
Collecting astunparse~=1.6.3
  Downloading astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting protobuf>=3.9.2
  Downloading protobuf-3.19.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
     |████████████████████████████████| 1.1 MB 7.0 MB/s 
Collecting keras-nightly~=2.5.0.dev
  Downloading keras_nightly-2.5.0.dev2021032900-py2.py3-none-any.whl (1.2 MB)
     |████████████████████████████████| 1.2 MB 17.6 MB/s 
Collecting grpcio~=1.34.0
  Downloading grpcio-1.34.1-cp39-cp39-manylinux2014_x86_64.whl (4.0 MB)
     |████████████████████████████████| 4.0 MB 17.1 MB/s 
Collecting wrapt~=1.12.1
  Downloading wrapt-1.12.1.tar.gz (27 kB)
Collecting tensorboard~=2.5
  Downloading tensorboard-2.7.0-py3-none-any.whl (5.8 MB)
     |████████████████████████████████| 5.8 MB 17.8 MB/s 
Requirement already satisfied: wheel~=0.35 in /data4/mkolopanis/src/anaconda/envs/dora/lib/python3.9/site-packages (from tensorflow==2.5.1->dora-exp-pipeline==0.0.9) (0.37.0)
Collecting keras-preprocessing~=1.1.2
  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
     |████████████████████████████████| 42 kB 4.6 MB/s 
Collecting typing-extensions~=3.7.4
  Downloading typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting tensorflow-estimator<2.6.0,>=2.5.0
  Downloading tensorflow_estimator-2.5.0-py2.py3-none-any.whl (462 kB)
     |████████████████████████████████| 462 kB 13.1 MB/s 
Collecting google-pasta~=0.2
  Downloading google_pasta-0.2.0-py3-none-any.whl (57 kB)
     |████████████████████████████████| 57 kB 9.7 MB/s 
Collecting flatbuffers~=1.12.0
  Downloading flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Collecting opt-einsum~=3.3.0
  Downloading opt_einsum-3.3.0-py3-none-any.whl (65 kB)
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Collecting h5py~=3.1.0
  Downloading h5py-3.1.0-cp39-cp39-manylinux1_x86_64.whl (4.4 MB)
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Collecting typeguard>=2.7
  Downloading typeguard-2.13.0-py3-none-any.whl (17 kB)
Collecting cloudpickle>=1.3
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Collecting dm-tree
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Collecting decorator
  Downloading decorator-5.1.0-py3-none-any.whl (9.1 kB)
Collecting imageio>=2.3.0
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Collecting tensorboard-plugin-wit>=1.6.0
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Collecting google-auth-oauthlib<0.5,>=0.4.1
  Downloading google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
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Collecting werkzeug>=0.11.15
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Collecting requests<3,>=2.21.0
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Collecting google-auth<3,>=1.6.3
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Collecting markdown>=2.6.8
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Collecting rsa<5,>=3.1.4
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Collecting pyasn1-modules>=0.2.1
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Collecting requests-oauthlib>=0.7.0
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Collecting pyasn1<0.5.0,>=0.4.6
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Collecting idna<4,>=2.5
  Downloading idna-3.3-py3-none-any.whl (61 kB)
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Collecting charset-normalizer~=2.0.0
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Collecting urllib3<1.27,>=1.21.1
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Collecting oauthlib>=3.0.0
  Downloading oauthlib-3.1.1-py2.py3-none-any.whl (146 kB)
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Building wheels for collected packages: dora-exp-pipeline, scikit-image, termcolor, wrapt
  Building wheel for dora-exp-pipeline (PEP 517) ... done
  Created wheel for dora-exp-pipeline: filename=dora_exp_pipeline-0.0.9-py3-none-any.whl size=45375 sha256=0195bafa0a39340d21fe1df41c3e7c7c320e8c87aeaa424706535ff2b053b901
  Stored in directory: /tmp/pip-ephem-wheel-cache-raarbl4h/wheels/f6/95/41/53ba3ab1b68b2c75895f11d9ae5e4dfbecd90887f2807aab21
  Building wheel for scikit-image (setup.py) ... done
  Created wheel for scikit-image: filename=scikit_image-0.17.2-cp39-cp39-linux_x86_64.whl size=12839423 sha256=699aaa0f92d76958756d16af382271bf441c142521fefb98b9b2d8e3b4e2b3ac
  Stored in directory: /home/mkolopanis/.cache/pip/wheels/7c/74/ce/c57a9d7b775a85b1aac1ade12c209148580f5ecf23560dd58b
  Building wheel for termcolor (setup.py) ... done
  Created wheel for termcolor: filename=termcolor-1.1.0-py3-none-any.whl size=4847 sha256=6be52e25d5ca0bab3ef74882125988b999cc5096768b547898a37a2555a4ca23
  Stored in directory: /home/mkolopanis/.cache/pip/wheels/b6/0d/90/0d1bbd99855f99cb2f6c2e5ff96f8023fad8ec367695f7d72d
  Building wheel for wrapt (setup.py) ... done
  Created wheel for wrapt: filename=wrapt-1.12.1-cp39-cp39-linux_x86_64.whl size=36916 sha256=054695dd1dca6f8a4aa6f175df6896b08cbaa6c8e3bc6dde8a3fb9a78a8dfc84
  Stored in directory: /home/mkolopanis/.cache/pip/wheels/98/23/68/efe259aaca055e93b08e74fbe512819c69a2155c11ba3c0f10
Successfully built dora-exp-pipeline scikit-image termcolor wrapt
Installing collected packages: urllib3, pyasn1, idna, charset-normalizer, six, rsa, requests, pyasn1-modules, oauthlib, cachetools, requests-oauthlib, google-auth, werkzeug, tensorboard-plugin-wit, tensorboard-data-server, python-dateutil, pyparsing, protobuf, Pillow, markdown, kiwisolver, grpcio, google-auth-oauthlib, cycler, click, absl-py, wrapt, typing-extensions, typeguard, tifffile, threadpoolctl, termcolor, tensorflow-estimator, tensorboard, snuggs, scipy, PyWavelets, pytz, pvl, opt-einsum, networkx, matplotlib, keras-preprocessing, keras-nightly, joblib, imageio, h5py, google-pasta, gast, flatbuffers, dm-tree, decorator, cloudpickle, cligj, click-plugins, attrs, astunparse, affine, tqdm, tensorflow-probability, tensorflow-addons, tensorflow, sklearn-som, scikit-learn, scikit-image, rasterio, PyYAML, planetaryimage, pandas, dora-exp-pipeline
Successfully installed Pillow-8.2.0 PyWavelets-1.1.1 PyYAML-5.4.1 absl-py-0.15.0 affine-2.3.0 astunparse-1.6.3 attrs-21.2.0 cachetools-4.2.4 charset-normalizer-2.0.7 click-8.0.3 click-plugins-1.1.1 cligj-0.7.2 cloudpickle-2.0.0 cycler-0.10.0 decorator-5.1.0 dm-tree-0.1.6 dora-exp-pipeline-0.0.9 flatbuffers-1.12 gast-0.4.0 google-auth-2.3.2 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.34.1 h5py-3.1.0 idna-3.3 imageio-2.9.0 joblib-1.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 kiwisolver-1.3.2 markdown-3.3.4 matplotlib-3.3.4 networkx-2.6.3 oauthlib-3.1.1 opt-einsum-3.3.0 pandas-1.1.5 planetaryimage-0.5.0 protobuf-3.19.0 pvl-1.3.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pyparsing-3.0.3 python-dateutil-2.8.2 pytz-2021.3 rasterio-1.2.6 requests-2.26.0 requests-oauthlib-1.3.0 rsa-4.7.2 scikit-image-0.17.2 scikit-learn-0.24.2 scipy-1.5.4 six-1.15.0 sklearn-som-1.1.0 snuggs-1.4.7 tensorboard-2.7.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.0 tensorflow-2.5.1 tensorflow-addons-0.13.0 tensorflow-estimator-2.5.0 tensorflow-probability-0.13.0 termcolor-1.1.0 threadpoolctl-3.0.0 tifffile-2021.10.12 tqdm-4.62.0 typeguard-2.13.0 typing-extensions-3.7.4.3 urllib3-1.26.7 werkzeug-2.0.2 wrapt-1.12.1
(dora) mkolopanis@enterprise [12:59:46] [~/src/dora] [master *]
-> %
Blank Env image==0.18.0 
(dora2) mkolopanis@enterprise [12:59:10] [~/src/dora] [master *]
-> % mamba list                      

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.15.3) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

# packages in environment at /home/mkolopanis/src/anaconda/envs/dora2:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             4.5                       1_gnu  
ca-certificates           2021.10.26           h06a4308_2  
certifi                   2021.10.8        py39h06a4308_0  
ld_impl_linux-64          2.35.1               h7274673_9  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h5101ec6_17  
libgomp                   9.3.0               h5101ec6_17  
libstdcxx-ng              9.3.0               hd4cf53a_17  
ncurses                   6.2                  he6710b0_1  
openssl                   1.1.1l               h7f8727e_0  
pip                       21.2.4           py39h06a4308_0  
python                    3.9.7                h12debd9_1  
readline                  8.1                  h27cfd23_0  
setuptools                58.0.4           py39h06a4308_0  
sqlite                    3.36.0               hc218d9a_0  
tk                        8.6.11               h1ccaba5_0  
tzdata                    2021e                hda174b7_0  
wheel                     0.37.0             pyhd3eb1b0_1  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.11               h7b6447c_3  
(dora2) mkolopanis@enterprise [12:59:18] [~/src/dora] [master *]
-> % pip install .  
Processing /data4/mkolopanis/src/dora
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
Collecting matplotlib==3.3.4
  Using cached matplotlib-3.3.4-cp39-cp39-manylinux1_x86_64.whl (11.5 MB)
Collecting numpy==1.19.5
  Using cached numpy-1.19.5-cp39-cp39-manylinux2010_x86_64.whl (14.9 MB)
Collecting scipy==1.5.4
  Using cached scipy-1.5.4-cp39-cp39-manylinux1_x86_64.whl (25.8 MB)
Collecting scikit-image==0.18.0
  Using cached scikit_image-0.18.0-cp39-cp39-manylinux1_x86_64.whl (28.9 MB)
Collecting scikit-learn==0.24.2
  Using cached scikit_learn-0.24.2-cp39-cp39-manylinux2010_x86_64.whl (23.8 MB)
Collecting Pillow==8.2.0
  Using cached Pillow-8.2.0-cp39-cp39-manylinux1_x86_64.whl (3.0 MB)
Collecting planetaryimage==0.5.0
  Using cached planetaryimage-0.5.0-py2.py3-none-any.whl (13 kB)
Collecting PyYAML==5.4.1
  Using cached PyYAML-5.4.1-cp39-cp39-manylinux1_x86_64.whl (630 kB)
Collecting pandas==1.1.5
  Using cached pandas-1.1.5-cp39-cp39-manylinux1_x86_64.whl (9.3 MB)
Collecting rasterio==1.2.6
  Using cached rasterio-1.2.6-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (19.2 MB)
Collecting tqdm==4.62.0
  Using cached tqdm-4.62.0-py2.py3-none-any.whl (76 kB)
Collecting tensorflow==2.5.1
  Using cached tensorflow-2.5.1-cp39-cp39-manylinux2010_x86_64.whl (454.5 MB)
Collecting tensorflow-probability==0.13.0
  Using cached tensorflow_probability-0.13.0-py2.py3-none-any.whl (5.4 MB)
Collecting tensorflow-addons==0.13.0
  Using cached tensorflow_addons-0.13.0-cp39-cp39-manylinux2010_x86_64.whl (679 kB)
Collecting sklearn-som==1.1.0
  Using cached sklearn_som-1.1.0-py3-none-any.whl (6.7 kB)
Collecting cycler>=0.10
  Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3
  Using cached pyparsing-3.0.3-py3-none-any.whl (96 kB)
Collecting kiwisolver>=1.0.1
  Using cached kiwisolver-1.3.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Collecting python-dateutil>=2.1
  Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2017.2
  Using cached pytz-2021.3-py2.py3-none-any.whl (503 kB)
Collecting six
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Collecting pvl
  Using cached pvl-1.3.0-py2.py3-none-any.whl (65 kB)
Collecting click-plugins
  Using cached click_plugins-1.1.1-py2.py3-none-any.whl (7.5 kB)
Requirement already satisfied: setuptools in /data4/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages (from rasterio==1.2.6->dora-exp-pipeline==0.0.9) (58.0.4)
Collecting click>=4.0
  Using cached click-8.0.3-py3-none-any.whl (97 kB)
Collecting snuggs>=1.4.1
  Using cached snuggs-1.4.7-py3-none-any.whl (5.4 kB)
Collecting affine
  Using cached affine-2.3.0-py2.py3-none-any.whl (15 kB)
Requirement already satisfied: certifi in /data4/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages (from rasterio==1.2.6->dora-exp-pipeline==0.0.9) (2021.10.8)
Collecting attrs
  Using cached attrs-21.2.0-py2.py3-none-any.whl (53 kB)
Collecting cligj>=0.5
  Using cached cligj-0.7.2-py3-none-any.whl (7.1 kB)
Collecting networkx>=2.0
  Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting imageio>=2.3.0
  Using cached imageio-2.10.1-py3-none-any.whl (3.3 MB)
Collecting tifffile>=2019.7.26
  Using cached tifffile-2021.10.12-py3-none-any.whl (175 kB)
Collecting PyWavelets>=1.1.1
  Using cached PyWavelets-1.1.1-cp39-cp39-manylinux1_x86_64.whl (4.3 MB)
Collecting joblib>=0.11
  Using cached joblib-1.1.0-py2.py3-none-any.whl (306 kB)
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-3.0.0-py3-none-any.whl (14 kB)
Requirement already satisfied: wheel~=0.35 in /data4/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages (from tensorflow==2.5.1->dora-exp-pipeline==0.0.9) (0.37.0)
Collecting termcolor~=1.1.0
  Using cached termcolor-1.1.0-py3-none-any.whl
Collecting h5py~=3.1.0
  Using cached h5py-3.1.0-cp39-cp39-manylinux1_x86_64.whl (4.4 MB)
Collecting astunparse~=1.6.3
  Using cached astunparse-1.6.3-py2.py3-none-any.whl (12 kB)
Collecting wrapt~=1.12.1
  Using cached wrapt-1.12.1-cp39-cp39-linux_x86_64.whl
Collecting grpcio~=1.34.0
  Using cached grpcio-1.34.1-cp39-cp39-manylinux2014_x86_64.whl (4.0 MB)
Collecting gast==0.4.0
  Using cached gast-0.4.0-py3-none-any.whl (9.8 kB)
Collecting keras-nightly~=2.5.0.dev
  Using cached keras_nightly-2.5.0.dev2021032900-py2.py3-none-any.whl (1.2 MB)
Collecting opt-einsum~=3.3.0
  Using cached opt_einsum-3.3.0-py3-none-any.whl (65 kB)
Collecting flatbuffers~=1.12.0
  Using cached flatbuffers-1.12-py2.py3-none-any.whl (15 kB)
Collecting six
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting keras-preprocessing~=1.1.2
  Using cached Keras_Preprocessing-1.1.2-py2.py3-none-any.whl (42 kB)
Collecting typing-extensions~=3.7.4
  Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting protobuf>=3.9.2
  Using cached protobuf-3.19.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.1 MB)
Collecting absl-py~=0.10
  Using cached absl_py-0.15.0-py3-none-any.whl (132 kB)
Collecting tensorflow-estimator<2.6.0,>=2.5.0
  Using cached tensorflow_estimator-2.5.0-py2.py3-none-any.whl (462 kB)
Collecting google-pasta~=0.2
  Using cached google_pasta-0.2.0-py3-none-any.whl (57 kB)
Collecting tensorboard~=2.5
  Using cached tensorboard-2.7.0-py3-none-any.whl (5.8 MB)
Collecting typeguard>=2.7
  Using cached typeguard-2.13.0-py3-none-any.whl (17 kB)
Collecting decorator
  Using cached decorator-5.1.0-py3-none-any.whl (9.1 kB)
Collecting cloudpickle>=1.3
  Using cached cloudpickle-2.0.0-py3-none-any.whl (25 kB)
Collecting dm-tree
  Using cached dm_tree-0.1.6-cp39-cp39-manylinux_2_24_x86_64.whl (94 kB)
Collecting imageio>=2.3.0
  Using cached imageio-2.9.0-py3-none-any.whl (3.3 MB)
Collecting werkzeug>=0.11.15
  Using cached Werkzeug-2.0.2-py3-none-any.whl (288 kB)
Collecting tensorboard-plugin-wit>=1.6.0
  Using cached tensorboard_plugin_wit-1.8.0-py3-none-any.whl (781 kB)
Collecting requests<3,>=2.21.0
  Using cached requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting google-auth<3,>=1.6.3
  Using cached google_auth-2.3.2-py2.py3-none-any.whl (155 kB)
Collecting tensorboard-data-server<0.7.0,>=0.6.0
  Using cached tensorboard_data_server-0.6.1-py3-none-manylinux2010_x86_64.whl (4.9 MB)
Collecting markdown>=2.6.8
  Using cached Markdown-3.3.4-py3-none-any.whl (97 kB)
Collecting google-auth-oauthlib<0.5,>=0.4.1
  Using cached google_auth_oauthlib-0.4.6-py2.py3-none-any.whl (18 kB)
Collecting rsa<5,>=3.1.4
  Using cached rsa-4.7.2-py3-none-any.whl (34 kB)
Collecting pyasn1-modules>=0.2.1
  Using cached pyasn1_modules-0.2.8-py2.py3-none-any.whl (155 kB)
Collecting cachetools<5.0,>=2.0.0
  Using cached cachetools-4.2.4-py3-none-any.whl (10 kB)
Collecting requests-oauthlib>=0.7.0
  Using cached requests_oauthlib-1.3.0-py2.py3-none-any.whl (23 kB)
Collecting pyasn1<0.5.0,>=0.4.6
  Using cached pyasn1-0.4.8-py2.py3-none-any.whl (77 kB)
Collecting idna<4,>=2.5
  Using cached idna-3.3-py3-none-any.whl (61 kB)
Collecting charset-normalizer~=2.0.0
  Using cached charset_normalizer-2.0.7-py3-none-any.whl (38 kB)
Collecting urllib3<1.27,>=1.21.1
  Using cached urllib3-1.26.7-py2.py3-none-any.whl (138 kB)
Collecting oauthlib>=3.0.0
  Using cached oauthlib-3.1.1-py2.py3-none-any.whl (146 kB)
Building wheels for collected packages: dora-exp-pipeline
  Building wheel for dora-exp-pipeline (setup.py) ... done
  Created wheel for dora-exp-pipeline: filename=dora_exp_pipeline-0.0.9-py3-none-any.whl size=45376 sha256=dd5d1c0c5abf33eeb39470e924095e487efebd5d81b4510473678f871fdd1a66
  Stored in directory: /tmp/pip-ephem-wheel-cache-5x_0eamm/wheels/f6/95/41/53ba3ab1b68b2c75895f11d9ae5e4dfbecd90887f2807aab21
Successfully built dora-exp-pipeline
Installing collected packages: urllib3, pyasn1, idna, charset-normalizer, six, rsa, requests, pyasn1-modules, oauthlib, cachetools, requests-oauthlib, google-auth, werkzeug, tensorboard-plugin-wit, tensorboard-data-server, python-dateutil, pyparsing, protobuf, Pillow, numpy, markdown, kiwisolver, grpcio, google-auth-oauthlib, cycler, click, absl-py, wrapt, typing-extensions, typeguard, tifffile, threadpoolctl, termcolor, tensorflow-estimator, tensorboard, snuggs, scipy, PyWavelets, pytz, pvl, opt-einsum, networkx, matplotlib, keras-preprocessing, keras-nightly, joblib, imageio, h5py, google-pasta, gast, flatbuffers, dm-tree, decorator, cloudpickle, cligj, click-plugins, attrs, astunparse, affine, tqdm, tensorflow-probability, tensorflow-addons, tensorflow, sklearn-som, scikit-learn, scikit-image, rasterio, PyYAML, planetaryimage, pandas, dora-exp-pipeline
Successfully installed Pillow-8.2.0 PyWavelets-1.1.1 PyYAML-5.4.1 absl-py-0.15.0 affine-2.3.0 astunparse-1.6.3 attrs-21.2.0 cachetools-4.2.4 charset-normalizer-2.0.7 click-8.0.3 click-plugins-1.1.1 cligj-0.7.2 cloudpickle-2.0.0 cycler-0.10.0 decorator-5.1.0 dm-tree-0.1.6 dora-exp-pipeline-0.0.9 flatbuffers-1.12 gast-0.4.0 google-auth-2.3.2 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.34.1 h5py-3.1.0 idna-3.3 imageio-2.9.0 joblib-1.1.0 keras-nightly-2.5.0.dev2021032900 keras-preprocessing-1.1.2 kiwisolver-1.3.2 markdown-3.3.4 matplotlib-3.3.4 networkx-2.6.3 numpy-1.19.5 oauthlib-3.1.1 opt-einsum-3.3.0 pandas-1.1.5 planetaryimage-0.5.0 protobuf-3.19.0 pvl-1.3.0 pyasn1-0.4.8 pyasn1-modules-0.2.8 pyparsing-3.0.3 python-dateutil-2.8.2 pytz-2021.3 rasterio-1.2.6 requests-2.26.0 requests-oauthlib-1.3.0 rsa-4.7.2 scikit-image-0.18.0 scikit-learn-0.24.2 scipy-1.5.4 six-1.15.0 sklearn-som-1.1.0 snuggs-1.4.7 tensorboard-2.7.0 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.0 tensorflow-2.5.1 tensorflow-addons-0.13.0 tensorflow-estimator-2.5.0 tensorflow-probability-0.13.0 termcolor-1.1.0 threadpoolctl-3.0.0 tifffile-2021.10.12 tqdm-4.62.0 typeguard-2.13.0 typing-extensions-3.7.4.3 urllib3-1.26.7 werkzeug-2.0.2 wrapt-1.12.1

(dora2) mkolopanis@excalibur [13:13:00] [~/src/dora] [master *]
-> % pytest 
========================================== test session starts ==========================================
platform linux -- Python 3.9.7, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /data4/mkolopanis/src/dora, configfile: pytest.ini
plugins: typeguard-2.13.0
collected 4 items                                                                                       

test/test_earth_time_series.py .                                                                  [ 25%]
test/test_earth_volcanoes_patches.py .                                                            [ 50%]
test/test_earth_volcanoes_pixels.py .                                                             [ 75%]
test/test_planetary.py F                                                                          [100%]

=============================================== FAILURES ================================================
________________________________________ TestPlanetary.test_run _________________________________________

self = <test_planetary.TestPlanetary testMethod=test_run>

    def test_run(self):
    
        config_file = 'test/planetary.config'
    
        # Run the experiment; also tests ability to parse config file
        start(config_file, self.outdir)
    
        # Check results for each algorithm
        for file_base in ['demud-k=5/selections-demud.csv',
                          'iforest-n_trees=100-fit_single_trees=False/'
                          'selections-iforest.csv',
                          'lrx-inner_window=3-outer_window=9-bands=1/'
                          'selections-lrx.csv',
                          'negative_sampling-percent_increase=20/'
                          'selections-negative_sampling.csv',
                          'pca-k=5/selections-pca.csv',
                          'random/selections-random.csv'
                          ]:
            correct_file = 'test/ref-results/planetary_rover/functional' \
                            '/%s' % file_base
            output_file = '%s/%s' % (self.outdir, file_base)
    
            # Check results against correct output
>           assert check_results(output_file, correct_file)
E           AssertionError: assert False
E            +  where False = check_results('/tmp/dora/test/planetary/demud-k=5/selections-demud.csv', 'test/ref-results/planetary_rover/functional/demud-k=5/selections-demud.csv')

test/test_planetary.py:49: AssertionError
----------------------------------------- Captured stdout call ------------------------------------------
Loading data_to_fit
Loading data_to_score
----------------------------------------- Captured stderr call ------------------------------------------
Feature extraction: 100%|██████████| 1/1 [00:00<00:00, 37.41it/s]
Feature extraction: 100%|██████████| 1/1 [00:00<00:00, 141.73it/s]
DEMUD: 100%|██████████| 8/8 [00:00<00:00, 1239.77it/s]s]
Negative Sampling: 100%|██████████| 100/100 [00:00<00:00, 44108.78it/s]
LRX: 100%|██████████| 8/8 [00:00<00:00, 311.95it/s]6,  5.60s/it]
Outlier detection: 100%|██████████| 6/6 [00:13<00:00,  2.25s/it]
=========================================== warnings summary ============================================
../../../../home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/pvl/collections.py:700
  /home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/pvl/collections.py:700: PendingDeprecationWarning: The pvl.collections.Units object is deprecated, and may be removed at the next major patch. Please use pvl.collections.Quantity instead.
    warnings.warn(

../../../../home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/planetaryimage/specialpixels.py:20: 12 warnings
  /home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/planetaryimage/specialpixels.py:20: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
    return numpy.fromstring(num, dtype=dtype)[0]

../../../../home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/tensorflow/python/autograph/impl/api.py:22
  /home/mkolopanis/src/anaconda/envs/dora2/lib/python3.9/site-packages/tensorflow/python/autograph/impl/api.py:22: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
    import imp

-- Docs: https://docs.pytest.org/en/stable/warnings.html
======================================== short test summary info ========================================
FAILED test/test_planetary.py::TestPlanetary::test_run - AssertionError: assert False
========================= 1 failed, 3 passed, 14 warnings in 162.77s (0:02:42) ==========================
@hannah-rae
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hannah-rae commented Oct 29, 2021 •
edited
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Thanks @mkolopanis for flagging this, I was able to reproduce the issue on my machine using conda too. While numpy is in the requirements list and is downloaded before scikit, I guess scikit wants it to be installed already. I also confirmed that using scikit-image==0.18.0 resolves the issue. (The failing pytest is a known issue unrelated to this, see #14.)

@stevenlujpl @wkiri @urebbapr Do you see any issues with upgrading to scikit-image==0.18.0? If not I can update the setup.py.

@urebbapr
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None of my code invokes scikit-image so all clear on my end.

@stevenlujpl
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stevenlujpl commented Oct 30, 2021 •
edited
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@hannah-rae We are using scikit-image for resizing images in FlattenedPixelValuesExtractor feature extractor. I would recommend testing the following function call and making sure the results are the same between scikit-image==0.17.2 and scikit-image==0.18.0.

from skimage import transform

# data is a 2d numpy array
resized_image = transform.resize(data, (height, width), anti_aliasing=True, preserve_range=True)

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@hannah-rae @mkolopanis @urebbapr @stevenlujpl